R: Leakage-Safe Modeling and Auditing for Genomic and Clinical Data

# Leakage-Safe Modeling and Auditing for Genomic and Clinical Data

## Documentation for package ‘bioLeak’ version 0.3.8

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

as_leaksplits | Convert a splitGraph split_spec into bioLeak splits
as_rsample | Convert LeakSplits to an rsample resample set
audit_batch_assoc | Batch / study association results from a LeakAudit
audit_batch_assoc-method | Batch / study association results from a LeakAudit
audit_duplicates | Near-duplicate pairs from a LeakAudit
audit_duplicates-method | Near-duplicate pairs from a LeakAudit
audit_info | Auxiliary information from a LeakAudit
audit_info-method | Auxiliary information from a LeakAudit
audit_leakage | Audit leakage and confounding
audit_leakage_by_learner | Audit leakage per learner
audit_perm_gap | Permutation-gap test results from a LeakAudit
audit_perm_gap-method | Permutation-gap test results from a LeakAudit
audit_report | Render an HTML audit report
audit_target_assoc | Target-leakage scan results from a LeakAudit
audit_target_assoc-method | Target-leakage scan results from a LeakAudit
benchmark_leakage_suite | Simulation benchmark matrix for leakage diagnostics
calibration_summary | Calibration diagnostics for binomial predictions
check_split_overlap | Check split overlap invariants
confounder_sensitivity | Confounder sensitivity summaries
cv_ci | Confidence intervals for cross-validated metrics
delta_lsi | Delta Leakage Sensitivity Index (Delta LSI)
dlsi_ci | BCa confidence interval from a LeakDeltaLSI
dlsi_ci-method | BCa confidence interval from a LeakDeltaLSI
dlsi_metric | Raw delta-metric estimate from a LeakDeltaLSI
dlsi_metric-method | Raw delta-metric estimate from a LeakDeltaLSI
dlsi_p_value | Sign-flip p-value from a LeakDeltaLSI
dlsi_p_value-method | Sign-flip p-value from a LeakDeltaLSI
dlsi_repeats | Per-repeat metric data frames from a LeakDeltaLSI
dlsi_repeats-method | Per-repeat metric data frames from a LeakDeltaLSI
dlsi_robust | Huber-robust delta_lsi point estimate from a LeakDeltaLSI
dlsi_robust-method | Huber-robust delta_lsi point estimate from a LeakDeltaLSI
dlsi_R_eff | Effective number of paired repeats from a LeakDeltaLSI
dlsi_R_eff-method | Effective number of paired repeats from a LeakDeltaLSI
dlsi_tier | Inference tier from a LeakDeltaLSI
dlsi_tier-method | Inference tier from a LeakDeltaLSI
fit_metrics | Per-fold metric data frame from a LeakFit
fit_metrics-method | Per-fold metric data frame from a LeakFit
fit_resample | Fit and evaluate with leakage guards over predefined splits
guard_ensure_levels | Ensure consistent categorical levels for guarded preprocessing
guard_fit | Fit leakage-safe preprocessing pipeline
guard_to_recipe | Convert guard preprocessing steps to a recipes recipe
impute_guarded | Leakage-safe data imputation via guarded preprocessing
LeakAudit-class | S4 Classes for bioLeak Pipeline
LeakClasses | S4 Classes for bioLeak Pipeline
LeakDeltaLSI-class | S4 Classes for bioLeak Pipeline
LeakFit-class | S4 Classes for bioLeak Pipeline
LeakSplits-class | S4 Classes for bioLeak Pipeline
make_split_plan | Create leakage-resistant splits
plot-method | Plot method for LeakAudit
plot-method | Plot method for LeakDeltaLSI
plot-method | Plot method for LeakFit
plot_calibration | Plot calibration curve for binomial predictions
plot_confounder_sensitivity | Plot confounder sensitivity
plot_dlsi_repeats | Plot per-repeat Delta_r values from a LeakDeltaLSI object
plot_fold_balance | Plot fold balance of class counts per fold
plot_overlap_checks | Plot overlap diagnostics between train/test groups
plot_perm_distribution | Plot permutation distribution for a LeakAudit object
plot_time_acf | Plot ACF of test predictions for time-series leakage checks
predict.GuardFit | Apply a fitted GuardFit transformer to new data
predict_guard | Apply a fitted GuardFit transformer to new data
print.LeakTune | Print a LeakTune object
show-method | S4 Classes for bioLeak Pipeline
show-method | Display summary for LeakAudit objects
show-method | Display summary for LeakFit objects
show-method | Display summary for LeakSplits objects
simulate_leakage_suite | Simulate leakage scenarios and audit results
summary.LeakAudit | Summarize a leakage audit
summary.LeakDeltaLSI | Summarize a LeakDeltaLSI object
summary.LeakFit | Summarize a LeakFit object
summary.LeakTune | Summarize a nested tuning result
tune_resample | Leakage-aware nested tuning with tidymodels